How do you figure out why species evolve a given trait?

An overview of the phylogentic
comparative approach:We know that eyespots have evolved multiple times. This is because we
observe the eyespots in several species with independent evolutionary
histories. Put simply, the caterpillars of several butterfly and moth species
have evolved the same solution for preventing or warding off attacks from
hungry predators (mostly birds). In evolutionary biology we call this convergent evolution.
As you might expect, there are also many cases where the eyespots of two
species will be similar because they both came from a common ancestor that had eyespots.As an evolutionary biologist, I am interested in deciphering how many times
has a given trait evolved, as well as why species evolve the traits that they
do. These questions are tightly linked because the more times a trait arises the
easier it is to detect a pattern that provides some insight into the selection
pressure that influenced the evolution of that trait. To examine these patterns
we use phylogenetic comparative analyses.
First, we quantify a character of interest (e.g., presence/absence of eyespots)
for several modern-day species, then for the same set of species we collect additional
data, such as another trait or habitat feature, that we think might push a
species to evolve the character of interest. Next, it is critical when
looking for evolutionary patterns that you control for the relatedness among the
species you are examining. Failing to account for species’ relatedness
invariably results in overestimating the strength of the true correlation between
the traits. Again, this is because we need to distinguish between two scenarios:
1) where two species share similar traits because they evolved from a common
ancestor that possessed both traits, and 2) where two species share similar traits because
evolution acted in a similar way on both species (i.e., convergent evolution). In
statistical terms, we need to correct for the lack of independence among related species (i.e., species that
share a common ancestor are not statistically independent data points). A
variety of techniques are now available to do this, all striving to account for
the lack of independence among related species. Essentially, they all boil down
to mapping our species of interest, and their associated traits, onto a phylogenetic tree. If many of the species
being compared possess the same set of traits because they share a common
ancestor (Scenario1) there is less evidence for a relationship between those traits,
whereas if many distantly related species share the same set of traits
(Scenario2) there is strong evidence for an evolutionary relationship between
them.

Case
study:The
evolution of warning coloration in the genus Papilio

There is now evidence which indicates that caterpillars are more likely
evolve aposematism
(i.e., bright colours and associated unpalatablity) when they live and feed in
areas where they are highly visible to predators, and not simply
because they feed on plants which contain toxins (Prudic et al. 2007 PNAS). But
how did the authors figure this out? They started by classifying the colour
patterns of existing Papilio genus caterpillars* (i.e., bird-dropping,
green, aposematic):

"Bird-dropping" Type

"Green" Type - Papilio canadensis

"Aposematic" or "Warning colour" Type - Papilio polyxenes

Next, they tested to see whether the aposematic trait correlated more strongly with the toxins of the corresponding food plant, or the leaf "archetecture" (i.e., broad vs. narrow leaves) of that food plant:

Narrow-leaved - Daucus carota

Broad-leaved - Populus tremuloides

Of the 59 Papilio species examined,
15 species fed on narrow-leaved plants, 12 were aposematic, and 11 were both aposematic and narrow-leaf feeders. Remember:
each species does not represent an independent data point because some
share the same set of traits because they share acommon
ancestor. The authors present genetic evidence which maps their 59 Papilio
species onto a phylogeny. It indicates that 7/12 aposematic species examined descended
from a common ancestral species that was both aposematic and fed on narrow-leaved plants. In
other words, these 7 species possess the same traits (warning colours and
narrow-leaved plant feeding) because of an evolutionary event that occurred in
their ancestor and not because they were subject to the same selection pressure and independatly evolved the traits.
The weight of evidence for the overall pattern is adjusted to account for this. Yet, their analysis also shows that aposematic larvae have evolved independently
about 6 times (within the 59 Papilio species examined). The remaining
5 aposematic species were not closely related to each other and 4 of
them feed on narrow leaved plants. In contrast, there was no clear relationship
between toxins of the food plant and the possession of warning colours. The
authors thus conclude that possession of warning colours was more closely
correlated to leaf architecture than plant toxin. This is an interesting result
and suggests that prey which can't hide effectively from their predators are
more likely to evolve toxins and showy colours to advertise their
unpalatability.I am currently using a similar approach to address the evolution of eyespots
in various groups of Lepidopteran caterpillars. I hope to have this done for
the Evolution2012 conference here in Ottawa, a joint conference between the
following societies: American Society of Naturalists (ASN), the Canadian Societyfor Ecology and Evolution (CSEE) the European Society for EvolutionaryBiology (ESEB), the Society for the Study of Evolution (SSE), and
the Society of Systematic Biologists (SSB).*Note Nearly all Papilio caterpillars share a common
"bird-dropping" colour pattern until the ~4th instar. Papilio
caterpillars with eyespots were classified as "green" in this study.